Table 1. Semantic knowledge bases containing information about organism characteristics.
| Name* | Description or Scope | Format | Pattern | Reference |
|---|---|---|---|---|
| Biodiversity | ||||
| Phenoscape† | Vertebrate morphology | OWL in RDF Blazegraph triplestore | EQ | [35,60] |
| EOL TraitBank†‡ | Internet aggregator of data about species | Neo4j | Character/Character State | [61,62] |
| Microbial Phenotypes Wiki‡ | Web-based community resource designed to display microbial phenotypes and the methods used to study them. | MediaWiki | Tabular, uses OMP [63] | [64] |
| PolyTraits‡ | Database on biological traits of polychaetes | Relational database | Character/Character State | [65,66] |
| TRY† | Global database of curated plant traits | Relational database | Map traits to TOP (EQ) [67] | [34] |
| FuTRES† | Functional traits of vertebrates | OWL in RDF triplestore | Measurement-Based quantitative data, trait definitions follow EQ pattern from OBAEQ | [68] |
| Planteome‡ | Plant genomics and phenomics | GAF and SOLR | EQ and DOS-DP | [69] |
| Global Plant Phenology† | Aggregator of plant phenological data | OWL and JSON | Measurement-Based quantitative and presence/absence data; EQ model | [70,71] |
| Semantic Morph·D·Base† | Repository for morphological data | OWL in RDF triplestore | Measurement-Based with connection to TBox: Phenotype Knowledge Graphs | [72–76] |
| TaxonWorks† | Web-based workbench for taxonomists and biodiversity scientists | PostgreSQL (relational database) | Class (OTU) or Measurement-Based (collection object). Qualitative, quantitative, statistical, media, gene, text, presence/absence, arbitrary triples (data attributes). | [77] |
| World Register of Marine Species‡ | Authoritative classification and catalogue of marine species | MS SQL relational database with trait module | Character/Character State | [78] |
| Agriculture | ||||
| Gramene‡ | Comparative functional genomics in crops and model plant species | MongoDB | JSON-like, using PO [79] | [80,81] |
| Sol Genomics Network‡ | Clade-oriented database dedicated to the biology of the Solanaceae family | Relational database (chado) | Tabular, dbxref to PO | [82,83] |
| GrainGenes‡ | Comprehensive resource for molecular and phenotypic information for wheat, barley, rye, and other related species, including oat. | Relational database (chado) | Tabular, using Plant TO [84] | [85,86] |
| Annex‡ | Cereals ontology | OWL | Measurement and Class-based | [87] |
| CassavaBase‡ | Genomic and phenomic resource for cassava | Relational database (chado) | Tabular, uses CO [88] | [89,90] |
| AgroLD‡ | Integrated data about commercially important plants | RDF triples | EQ and DOS-DP | [91] |
| Biomedicine and Model Organisms | ||||
| Monarch Initiative, uPheno, and Human Phenotype Ontology‡ | Integrator of cross species genotype-phenotype data including human phenotypes and their relationship to diseases | OWL | EQ and DOS-DP | [28,92,93] |
| MGI‡ | Mouse genomic and phenomic resource | OWL and OBO | EQ and DOS-DP | [94,95] |
| WormBase‡ | Nematode genomic and phenomic resource | OWL and OBO | EQ and DOS-DP | [96,97] |
| TAIR‡ | Arabidopsis genomic and phenomic resource | OWL and OBO | EQ and DOS-DP | [98,99] |
| FlyBase‡ | Fruit fly genomic and phenomic resource | OWL and OBO | EQ and DOS-DP | [100,101] |
| XenBase‡ | Xenopus genomic and phenomic resource | OWL and OBO | EQ and DOS-DP | [102,103] |
| ZFIN‡ | Zebrafish genomic and phenomic resource | OWL and OBO | EQ and DOS-DP | [104,105] |
| Saccharomyces Genome Database‡ | Comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae | PostgreSQL | Tabular, uses APO [106] | [107] |
| RGD ‡ | Structured and standardized data for 8 species (rat, mouse, human, chinchilla, bonobo, 13-lined ground squirrel, dog, and pig) | Relational database (chado), GAF, and OBO | Qualitative, links QTLs to multiple OBO phenotype ontologies | [108,109] |
*To be included in this table, a resource must contain annotations linking traits to organisms, use a phenotype ontology, and not require login credentials.
†Includes phenotype data reported at the individual specimen level.
‡Includes phenotype data reported at the group level.
APO, Ascomycete Phenotype Ontology; CO, Crop Ontology; DOS-DP, Dead Simple Ontology Design Pattern; EQ, Entity–Quality; GAF, GO Annotation File format; OBAEQ, Ontology of Biological Attributes-Entity Quality; OBO, Open Biomedical Ontologies format; OMP, Ontology of Microbial Phenotypes; OWL, Web Ontology Language; OTU, Operational Taxonomic Units; PO, Plant Ontology; QTL, Quantitative Trait Locus; RDF, Resource Description Framework; RGD, Rat Genome Database; TO, Trait Ontology; TOP, Thesaurus of Plant Characteristics.